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The story is told in the Vana Parva of the Mahabharata. When Shishupala was born, he had three eyes and four arms, which terrified his parents, the king and queen of Chedi. Then an invisible voice from the heavens sounded from the heavens and said this:

This thy son, O king, that hath been born will become both fortunate and superior in strength. Therefore thou hast no fear from him. Indeed cherish the child without anxiety. He will not die (in childhood). His time is not yet come. He that will slay him with weapons hath also been born.

His parents were worried and asked the voice who would be the one that would kill Shishupala, and it answered:

He upon whose lap this child being placed the superfluous arms of his will fall down upon the ground like a pair of five-headed snakes, and at the sight of whom his third eye on the forehead will disappear, will be his slayer[.]

So his parents called all the kings of the world to Chedi and put the child on each of their their laps to see which one would be the slayer. Finally Krishna and Balarama (who were children at the time) came, as they were nephews of the queen of Chedi. (The queen of Chedi was the sister of Krishna's father Vasudeva). As soon as Krishna put Shishupala in his lap, Shishupala's extra arms fell off and his third eye disappeared. So the queen of Chedi realized that Krishna was the one prophesied to kill Shishupala, and she asked him "O thou of great strength, thou wilt have to pardon the offences of Sisupala for my sake. O tiger of the Yadu race. Know O lord, even this is the boon that I ask." And Krishna responded "O aunt, even when he will deserve to be slain, I will pardon an hundred offences of his. Grieve thou not."

But when he grew up Shishupala found a way to commit a hundred offenses, making his last offenses at Yudishtra's Rajasuya Yagna, and in the middle of the Yagna, in front of all the kings present, Krishna killed Shishupala with the Sudarshana Chakra, saying this:

Listen ye lords of earth, why this one had hitherto been pardoned by me. As asked by his mother, a hundred offences (of his) were to be pardoned by me. Even this was the boon she had asked, and even this I granted her. That number, ye kings, hath become full. I shall now slay him in your presence, ye monarchs.